LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# 2d LJ obstacle flow

dimension	2
boundary	p s p

atom_style	atomic
neighbor	0.3 bin
neigh_modify	delay 5

# create geometry

lattice		hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region		box block 0 40 0 10 -0.25 0.25
create_box	3 box
Created orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
  1 by 1 by 1 MPI processor grid
create_atoms	1 box
Created 840 atoms
  Time spent = 0.0004704 secs

mass		1 1.0
mass		2 1.0
mass		3 1.0

# LJ potentials

pair_style	lj/cut 1.12246
pair_coeff	* * 1.0 1.0 1.12246

# define groups

region	        1 block INF INF INF 1.25 INF INF
group		lower region 1
120 atoms in group lower
region		2 block INF INF 8.75 INF INF INF
group		upper region 2
120 atoms in group upper
group		boundary union lower upper
240 atoms in group boundary
group		flow subtract all boundary
600 atoms in group flow

set		group lower type 2
  120 settings made for type
set		group upper type 3
  120 settings made for type

# initial velocities

compute	        mobile flow temp
velocity	flow create 1.0 482748 temp mobile
fix		1 all nve
fix		2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify	2 temp mobile

# Poiselle flow

velocity	boundary set 0.0 0.0 0.0
fix		3 lower setforce 0.0 0.0 0.0
fix		4 upper setforce 0.0 NULL 0.0
fix		5 upper aveforce 0.0 -0.5 0.0
fix		6 flow addforce 1.0 0.0 0.0

# 2 obstacles

region		void1 sphere 10 4 0 3
delete_atoms	region void1
Deleted 36 atoms, new total = 804
region		void2 sphere 20 7 0 3
delete_atoms	region void2
Deleted 35 atoms, new total = 769

fix		7 flow indent 100 sphere 10 4 0 4
fix		8 flow indent 100 sphere 20 7 0 4
fix		9 all enforce2d

# Run

timestep	0.003
thermo		1000
thermo_modify	temp mobile
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)

#dump		1 all atom 100 dump.obstacle

#dump		2 all image 500 image.*.jpg type type #		zoom 1.6 adiam 1.5
#dump_modify	2 pad 5

#dump		3 all movie 500 movie.mpg type type #		zoom 1.6 adiam 1.5
#dump_modify	3 pad 5

run		25000
Neighbor list info ...
  update every 1 steps, delay 5 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.42246
  ghost atom cutoff = 1.42246
  binsize = 0.71123, bins = 73 32 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.055 | 3.055 | 3.055 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
       0    1.0027471            0            0   0.68849216   0.46317653    1143.0857 
    1000            1  -0.33689286            0   0.34971312    1.2905426    1286.7728 
    2000            1  -0.36746164            0   0.31914434    1.1668828      1313.44 
    3000            1  -0.52004759            0   0.16655839     1.417774     1324.489 
    4000            1   -0.5052153            0   0.18139068    1.4877209    1370.8743 
    5000            1  -0.49501138            0    0.1915946    1.2415582    1408.4993 
    6000            1  -0.45834057            0   0.22826542    1.2577643    1433.2191 
    7000            1  -0.44788351            0   0.23872247    1.1057853    1452.7011 
    8000            1  -0.42511924            0   0.26148674    1.1445522    1453.2588 
    9000            1  -0.35807547            0   0.32853051    1.0527564    1449.2608 
   10000            1  -0.38692228            0    0.2996837    1.0338935    1447.9561 
   11000            1  -0.38893457            0   0.29767141    1.0095645    1451.1231 
   12000            1  -0.35706485            0   0.32954114    1.0796623    1453.0879 
   13000            1  -0.39551125            0   0.29109474    1.0390286    1453.2992 
   14000            1  -0.38153043            0   0.30507555   0.98105926    1452.5639 
   15000            1  -0.38762689            0   0.29897909    1.1442417    1452.0174 
   16000            1   -0.3685331            0   0.31807289    1.0032132     1458.431 
   17000            1  -0.36299809            0   0.32360789   0.93727845    1460.2986 
   18000            1  -0.35752931            0   0.32907667   0.98337283     1458.583 
   19000            1  -0.38350344            0   0.30310254    1.0148373    1458.9749 
   20000            1  -0.35659703            0   0.33000895    1.0264431    1460.0031 
   21000            1  -0.36878002            0   0.31782596    1.0877739    1455.1053 
   22000            1  -0.37986917            0   0.30673681     1.129754    1455.0258 
   23000            1  -0.39249509            0   0.29411089   0.97187435    1459.6771 
   24000            1  -0.33410442            0   0.35250156   0.93960021    1463.5903 
   25000            1  -0.37437615            0   0.31222983    0.9644765    1464.9391 
Loop time of 1.98053 on 1 procs for 25000 steps with 769 atoms

Performance: 3271856.949 tau/day, 12622.905 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.46219    | 0.46219    | 0.46219    |   0.0 | 23.34
Neigh   | 0.17       | 0.17       | 0.17       |   0.0 |  8.58
Comm    | 0.029093   | 0.029093   | 0.029093   |   0.0 |  1.47
Output  | 0.00041389 | 0.00041389 | 0.00041389 |   0.0 |  0.02
Modify  | 1.22       | 1.22       | 1.22       |   0.0 | 61.60
Other   |            | 0.09888    |            |       |  4.99

Nlocal:    769 ave 769 max 769 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    45 ave 45 max 45 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    1618 ave 1618 max 1618 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1618
Ave neighs/atom = 2.10403
Neighbor list builds = 1622
Dangerous builds = 0
Total wall time: 0:00:01
